From chemistry-request@server.ccl.net Thu Jan 23 05:47:55 2003 Received: from bute.st-andrews.ac.uk ([138.251.12.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NAlse03913 for ; Thu, 23 Jan 2003 05:47:54 -0500 Received: from superintendentchalmers.st-andrews.ac.uk (bmspc-glt2-9 [138.251.94.76]) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with ESMTP id KAA16685 for ; Thu, 23 Jan 2003 10:38:39 GMT Message-Id: <5.1.1.6.0.20030123103446.00a6f2c8@bute.st-andrews.ac.uk> X-Sender: im17@bute.st-andrews.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Thu, 23 Jan 2003 10:49:48 +0000 To: chemistry@ccl.net From: "Ibrahim M.Moustafa" Subject: GRASP electrostatic potential Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL users; When calculating the electrostatic potential surface in GRASP for a macromolecule, the surface can be color coded according to the absolute values of the calculated potential. Does any body know which unit is used in GRASP calculation?. I always see in papers the ESP surfaces are colored with codes between values of (1KT) and (-1KT), is it the unit used in GRASP calculations? or how can we convert the unit in GRASP to KT unit? Appreciated your help. Ibrahim Ibrahim M.Mostafa Center for Biomolecular Sciences, Molecular Sciences Building, North Haugh,St.Andrews, Fife,KY16 9ST, Scotland,U.K. Tel. +44-1334-467257 Fax +44-1334-462595 e-mail: im17@st-Andrews.ac.uk From chemistry-request@server.ccl.net Thu Jan 23 05:42:15 2003 Received: from dedalus.lcc.ufmg.br ([150.164.65.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NAgFe03706 for ; Thu, 23 Jan 2003 05:42:15 -0500 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with ESMTP id IAA15502; Thu, 23 Jan 2003 08:41:23 -0200 Date: Thu, 23 Jan 2003 08:41:22 -0200 (BDB) From: andre mauricio de oliveira X-X-Sender: amolive@dedalus To: Atchara Wijitkosoom cc: "chemistry@ccl.net" Subject: Re: CCL:About missing residues In-Reply-To: <3E2F34C5.3178CE75@mercury.hec.utah.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr Atchara, SwissPDB-Viewer (http://www.expasy.ch/spdbv) is able to analyse the protein structure and add missing residues based on homology requirements. Regards. On Wed, 22 Jan 2003, Atchara Wijitkosoom wrote: > To whom it may concern, > > Does anybody know the program that be able to add some missing residues > in protein? Thanks in advance. > > Yours, > Atchara > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@server.ccl.net Thu Jan 23 01:13:56 2003 Received: from mail014.syd.optusnet.com.au ([210.49.20.172]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0N6Dte15759 for ; Thu, 23 Jan 2003 01:13:55 -0500 Received: from co3022556-a (c18842.eburwd1.vic.optusnet.com.au [210.49.181.184]) by mail014.syd.optusnet.com.au (8.11.1/8.11.1) with ESMTP id h0N6DrH02979 for ; Thu, 23 Jan 2003 17:13:54 +1100 Message-ID: <200301231713540031.01E3AAB9@mail.eburwd1.vic.optushome.com.au> X-Mailer: Calypso Version 3.30.00.00 (4) Date: Thu, 23 Jan 2003 17:13:54 +1100 From: "SciMetrics" To: chemistry@ccl.net Subject: SciPredict, Chemical Prediction Software Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====_10433024343728=_" --=====_10433024343728=_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable SciPredict is now available on www.scimetrics.com Download the program and you will be able to access the Vapor Pressure= model for a 10 days free trial. Models available for purchase are Vapor Pressure, LogP, Henry's law and= Water Solubility. If you wish to be removed from this email list please reply with Remove in= the subject line. If you have received this email twice please let me know and I will fix it. Send queries and comments to me at: Dr Frank Burden SciMetrics 23 Harrow Street Blackburn South VIC 3130 Australia frank.burden@scimetrics.com --=====_10433024343728=_ Content-Type: text/html; charset="us-ascii"
SciPredict is now available on www.scimetrics.com
 
Download the program and you will be able to access the Vapor Pressure model for a 10 days free trial.
Models available for purchase are Vapor Pressure, LogP, Henry's law and Water Solubility.
 
If you wish to be removed from this email list please reply with Remove in the subject line.
 
If you have received this email twice please let me know and I will fix it.
 
Send queries and comments to me at:
 
Dr Frank Burden
SciMetrics
23 Harrow Street
Blackburn South
VIC 3130   Australia
frank.burden@scimetrics.com
--=====_10433024343728=_-- From chemistry-request@server.ccl.net Thu Jan 23 05:12:33 2003 Received: from galileo.fis.unipr.it ([192.135.11.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NACXe02567 for ; Thu, 23 Jan 2003 05:12:33 -0500 Received: from fis.unipr.it (pc116.fis.unipr.it [160.78.33.116]) by galileo.fis.unipr.it (8.11.6/8.11.6) with ESMTP id h0NACQ501348; Thu, 23 Jan 2003 11:12:26 +0100 Message-ID: <3E2FBFCC.5080303@fis.unipr.it> Date: Thu, 23 Jan 2003 11:11:24 +0100 From: Eugenia Polverini Organization: Dip. Fisica Universita' di Parma User-Agent: Mozilla/5.0 (Windows; U; Win 9x 4.90; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Atchara Wijitkosoom , CCL Subject: Re: CCL:About missing residues References: <3E2F34C5.3178CE75@mercury.hec.utah.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi! SwissPdbViewer can do this, when you load a molecule. http://www.expasy.org/spdbv/ Cheers Eugenia Atchara Wijitkosoom wrote: >To whom it may concern, > >Does anybody know the program that be able to add some missing residues >in protein? Thanks in advance. > >Yours, >Atchara > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > -- Eugenia Polverini, Ph.D. Dept. of Physics University of Parma Parco Area delle Scienze, 7/A 43100 Parma ITALY Phone: +39 0521 905254 Fax: +39 0521 905223 E-Mail: eugenia.polverini@fis.unipr.it From chemistry-request@server.ccl.net Thu Jan 23 09:33:32 2003 Received: from smtp.uibk.ac.at ([138.232.1.142]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NEXVe12263 for ; Thu, 23 Jan 2003 09:33:31 -0500 Received: from localhost (web-mail2.uibk.ac.at [138.232.1.226]) by smtp.uibk.ac.at (8.12.5/8.12.5/F1) with ESMTP id h0NEXV6l000384 for ; Thu, 23 Jan 2003 15:33:31 +0100 Received: from 62.47.211.90 ( [62.47.211.90]) as user c72409@mail1.uibk.ac.at by web-mail2.uibk.ac.at with HTTP; Thu, 23 Jan 2003 15:33:31 +0100 Message-ID: <1043332411.3e2ffd3b22f1b@web-mail2.uibk.ac.at> Date: Thu, 23 Jan 2003 15:33:31 +0100 From: Hannes Loeffler To: chemistry@ccl.net Subject: which solvents available for CHARMM MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 62.47.211.90 X-Spam-Score: -1.3 () SPAM_PHRASE_00_01,USER_AGENT,USER_AGENT_IMP X-Scanned-By: MIMEDefang 2.26 at uibk.ac.at (www . roaringpenguin . com / mimedefang) Hi, I would like to know which other solvents besides water (small alcohols, ammines/ammonia, sulfoxides, nitriles, etc.) are available for the CHARMM force field. TIA, Hannes. From chemistry-request@server.ccl.net Thu Jan 23 11:08:58 2003 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NG8we15847 for ; Thu, 23 Jan 2003 11:08:58 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #13) id 18bjuT-0006DR-00; Thu, 23 Jan 2003 17:08:57 +0100 Message-ID: <3E301393.20006@mpi-bpc.mpg.de> Date: Thu, 23 Jan 2003 17:08:51 +0100 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en, ro MIME-Version: 1.0 To: VMD , CCL Subject: visualizing Delphi output (electrostatic potential) Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Friends, I have run Delphi jobs and I got ".phi" files. I also got from Delphi runs a files "data", "ARCDAT". Could somebody explain very shortly something about "data" and "ARCDAT"files? Also I would like to visualize the electrostatic potential calculated using VMD, gOPENMOL or some other software. Could somebody give some hints about how to do that? For vmders, Is VMD able to do this type of job or shell I use something else? I do not have installed Delphi on the machine that I want to visualize the data so dont know if the scripts from the library are applicable. All that I have is the output files from Delphi. Thanks a lot in advance for any kind of help, Best regards, vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@server.ccl.net Thu Jan 23 11:23:09 2003 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NGN9e16274 for ; Thu, 23 Jan 2003 11:23:09 -0500 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id h0NGN9V08141; Thu, 23 Jan 2003 10:23:09 -0600 (CST) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id KAA15915; Thu, 23 Jan 2003 10:23:09 -0600 (CST) Date: Thu, 23 Jan 2003 10:23:09 -0600 From: John Stone To: Vlad Cojocaru Cc: VMD , CCL Subject: Re: visualizing Delphi output (electrostatic potential) Message-ID: <20030123102305.D15738@geneseo.ks.uiuc.edu> Mail-Followup-To: John Stone , Vlad Cojocaru , VMD , CCL References: <3E301393.20006@mpi-bpc.mpg.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <3E301393.20006@mpi-bpc.mpg.de> User-Agent: Mutt/1.3.19i Dear Vlad, There are two VMD scripts available which may be of interest to you since you have access to Delphi. One is "potsel" which calculates potential for an atom selection in VMD, and the other is "potsurf" which colors a surface representation in VMD by the potential values supplied by Delphi. These two scripts should be a good starting point for you to get VMD working with Delphi. The two scripts are here: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/potsel/ http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/potsurf/ Along the same lines, I believe that Nathan Baker's APBS package comes with some scripts to allow it to work with VMD. It is available for free, and they've got a web portal setup for running jobs on the NPACI machines: http://agave.wustl.edu/apbs/ Thanks, John Stone vmd@ks.uiuc.edu On Thu, Jan 23, 2003 at 05:08:51PM +0100, Vlad Cojocaru wrote: > Dear Friends, > I have run Delphi jobs and I got ".phi" files. I also got from > Delphi runs a files "data", "ARCDAT". Could somebody explain very > shortly something about "data" and "ARCDAT"files? Also I would like to > visualize the electrostatic potential calculated using VMD, gOPENMOL or > some other software. Could somebody give some hints about how to do that? > > For vmders, > Is VMD able to do this type of job or shell I use something else? I > do not have installed Delphi on the machine that I want to visualize the > data so dont know if the scripts from the library are applicable. All > that I have is the output files from Delphi. > > Thanks a lot in advance for any kind of help, > Best regards, > vlad > > -- > Vlad Cojocaru > Max Planck Institute for Biophysical Chemistry > Department: 060 > Am Fassberg 11, 37077 Goettingen, Germany > tel: ++49-551-201.1327 > e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de > home tel: ++49-551-9963204 > > -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@server.ccl.net Thu Jan 23 13:26:04 2003 Received: from f04n01.cac.psu.edu ([128.118.141.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NIQ3e20485 for ; Thu, 23 Jan 2003 13:26:04 -0500 Received: from psu.edu (cornea.chem.psu.edu [128.118.172.87]) by f04n01.cac.psu.edu (8.9.3/8.9.3) with ESMTP id NAA88364 for ; Thu, 23 Jan 2003 13:25:59 -0500 Message-ID: <3E3033B7.EFD7D93C@psu.edu> Date: Thu, 23 Jan 2003 13:26:02 -0500 From: Ed Brothers Reply-To: enb108@psu.edu Organization: PSU Merz Group X-Mailer: Mozilla 4.61 (Macintosh; I; PPC) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net Subject: Frequency conversion factors. Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit I am currently trying to calculate molecular frequencies, and am having some difficulty with the unit conversion. The hessian is in Hartrees*borh^-2, and if you diagonalize it the eigenvalues are 4*Pi^2*v^2, where v are the harmonic frequencies. Using the eigenvalues and the speed of light you can get v in cm^-1. However, codes I have examined involve other conversion factors for the frequencies, and I was wondering what those were, and where do they come from. Thanks very much for your help, Ed Brothers Merz Group Penn State From chemistry-request@server.ccl.net Thu Jan 23 11:08:43 2003 Received: from hpserv.imim.es ([193.144.6.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NG8ge15834 for ; Thu, 23 Jan 2003 11:08:42 -0500 Received: by hpserv.imim.es with Internet Mail Service (5.5.2656.59) id ; Thu, 23 Jan 2003 17:12:06 +0100 Received: from imim.es (prb0116.imim.es [193.146.190.158]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2656.59) id CPKKH0N7; Thu, 23 Jan 2003 17:12:02 +0100 From: =?iso-8859-1?Q?=22Gregori_Puigjan=E9=2C_Elisabet=22?= To: chemistry@ccl.net Message-ID: <3E301239.7D9662A7@imim.es> Date: Thu, 23 Jan 2003 17:03:05 +0100 X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.7-10 i686) X-Accept-Language: en MIME-Version: 1.0 Subject: Basis functions in GAMESS Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi I'm just begining in computational chemistry and my question may seem naive, but I have a problem running GAMESS with a selenium atom. The program doesn't seem to like me to ask for a 6.311 *+ basis function. The problem is in the 311 part, because if I change it to 31 it works, but with 311 the program says: ILLEGAL EXTENDED BASIS FUNCTION REQUESTED. My question is: does it have any sense to ask for a 6.311 basis function and, it it has, how can I incorporate a function basis in my GAMESS calculus? thanks in advance! Elisabet Gregori From chemistry-request@server.ccl.net Thu Jan 23 12:33:40 2003 Received: from mrelay.inscc.utah.edu ([155.101.3.60]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NHXde18523 for ; Thu, 23 Jan 2003 12:33:39 -0500 Received: from mail.inscc.utah.edu (mail.inscc.utah.edu [155.101.3.59]) by mrelay.inscc.utah.edu (8.9.2/8.9.2) with ESMTP id KAA08550; Thu, 23 Jan 2003 10:33:39 -0700 (MST) Received: from mercury.hec.utah.edu (tntpc2.hec.utah.edu [155.101.19.38]) by mail.inscc.utah.edu with ESMTP id KAA02981; Thu, 23 Jan 2003 10:33:38 -0700 (MST) Message-ID: <3E302772.1E81AA2F@mercury.hec.utah.edu> Date: Thu, 23 Jan 2003 10:33:38 -0700 From: Atchara Wijitkosoom X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: "Nicolas Ferre'" , "chemistry@ccl.net" Subject: Re: CCL:About missing residues References: <3E2F34C5.3178CE75@mercury.hec.utah.edu> <3E2FA026.3F4A973B@unisi.it> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Here is the response from many people about adding the missing residues. Hope it may be helpful for other people. Atchara > > >> At 05:18 PM 1/22/03 -0700, you wrote: >> >To whom it may concern, >> > >> >Does anybody know the program that be able to add some missing residues >> >in protein? Thanks in advance. > > > Anyway, I'd like you to post (at least to me) a summary of your > responses. > Thanks. > > Nicolas > 1. The Biopolymers module of SYBYL (Tripos Inc., St. Louis, MO) should handle the task. 2. In principle, Molden should be able to do it but my own experience is that it does not work in all cases. 3. The crdgrow programm which is part of AMBER7 can do this (its automated and easy) if parts of a residue are missing (mostly used for hydrogens, but works for heavy atoms as well) If whole parts of a chain are missing, you can try to use MODELLER, a friend of mine used it to build missing loops. 4. Jackal. http://trantor.bioc.columbia.edu/~xiang/jackal/#profix 5. SwissPdbViewer can do this, when you load a molecule. http://www.expasy.org/spdbv/ 6. Even Leap can do that. But you have to specify at least 3 atoms from each residue that you want to add in the pdb file (with coordinates). Alternatively you can do it with any other modeling software by building a small peptide that contains the new residues plus 1-2 residues from the protein (the ones adjacent to the new ones). Then you can run some minimization with positional restraints on the common residues and then do an rms fit with them and write a pdb file with both molecule and remove the atoms that appear twice. From chemistry-request@server.ccl.net Thu Jan 23 13:23:29 2003 Received: from smtp.csc.fi ([193.166.0.106]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NINTe20423 for ; Thu, 23 Jan 2003 13:23:29 -0500 Received: from ISOSIRRI (rhols63.adsl.netsonic.fi [194.29.198.63]) by smtp.csc.fi (CSC-Sendmail) with ESMTP id h0NINNa5003970 for ; Thu, 23 Jan 2003 20:23:23 +0200 From: "Leif Laaksonen" To: "'CCL'" Subject: RE: visualizing Delphi output (electrostatic potential) Date: Thu, 23 Jan 2003 20:23:24 +0200 Message-ID: <001701c2c30c$8481d400$ba1c7b0a@ISOSIRRI> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4510 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 In-Reply-To: <3E301393.20006@mpi-bpc.mpg.de> Importance: Normal X-Scanned-By: MIMEDefang 2.23 (www . roaringpenguin . com / mimedefang) Vlad, Look into the gOpenMol util/ directory where you find the delphi2plt program for converting phi files to plt files for gOpenMol. Regards, -leif -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net] On Behalf Of Vlad Cojocaru Sent: Thursday, January 23, 2003 6:09 PM To: VMD; CCL Subject: CCL:visualizing Delphi output (electrostatic potential) Dear Friends, I have run Delphi jobs and I got ".phi" files. I also got from Delphi runs a files "data", "ARCDAT". Could somebody explain very shortly something about "data" and "ARCDAT"files? Also I would like to visualize the electrostatic potential calculated using VMD, gOPENMOL or some other software. Could somebody give some hints about how to do that? For vmders, Is VMD able to do this type of job or shell I use something else? I do not have installed Delphi on the machine that I want to visualize the data so dont know if the scripts from the library are applicable. All that I have is the output files from Delphi. Thanks a lot in advance for any kind of help, Best regards, vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Jan 23 15:01:06 2003 Received: from mail.ccmsi.us ([143.132.103.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NK13e23708 for ; Thu, 23 Jan 2003 15:01:06 -0500 Received: from Falcon [10.30.6.25] by mail.ccmsi.us (SMTPD32-7.13) id AA00B730140; Thu, 23 Jan 2003 14:01:04 -0600 Message-ID: <00d001c2c31a$28d32f10$19061e0a@ccmsi.us> From: "Yevgeniy Podolyan" To: Subject: 03.03.28 3rd Southern School on Computational Chemistry, Orange Beach, AL, USA Date: Thu, 23 Jan 2003 14:01:04 -0600 Organization: Jackson State University MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Dear Colleague: We invite you to participate in the 3rd Southern School on Computational Chemistry organized together by the members of the NSF-EPSCOR Computational Chemistry Cluster, NSF-CREST Computational Center for Molecular Structure and Interactions, and the Army High Performance Computing Research Center. The meeting will be held at the Winfield Resort Hotel in beautiful Orange Beach, Alabama (next to Pensacola, FL) on March 28 and 29, 2002 (Friday 2 p.m. - Saturday 10 p.m.). There will be two formal lectures by Dr. Peter Politzer from University of New Orleans and Dr. Andrzej Sokalski from Wroclaw University of Technology. In addition, we are planning 20-30-minute oral presentations of senior investigators and posters from the students. These presentations will cover all areas of computational and quantum chemistry. A special session on High Performance Computing on Large Molecular Systems is scheduled for the Friday afternoon. We will publish a volume of proceeding with abstracts and a special issue of "Structural Chemistry" with selected papers from the meeting. Please email your abstracts by March 1, 2003 to Dr. Y. Podolyan podolyan@ccmsi.us (up to 4 pages in Microsoft Word format) with indication if you prefer oral or poster presentation and a file with your picture. These pictures will be included in the conference materials along with the list of participants. You can also register online at http://sscc.ccmsi.us. The conference fee, which includes meals (Friday dinner through Sunday breakfast), is $125. I hope to see you at our School. Jerzy Leszczynski From chemistry-request@server.ccl.net Thu Jan 23 17:50:59 2003 Received: from jacobus.chem.smu.edu ([129.119.201.27]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0NMoxe29365 for ; Thu, 23 Jan 2003 17:50:59 -0500 Received: from localhost (zmz@localhost) by jacobus.chem.smu.edu (8.11.6/8.11.6) with ESMTP id h0NMp6K28128 for ; Thu, 23 Jan 2003 16:51:06 -0600 Date: Thu, 23 Jan 2003 16:51:06 -0600 (CST) From: Pearl Zheng To: Subject: Energy minimization after docking In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer, Recently I want to perform energy minimization on the "best" predicted docked structures to refine the orientation of the substrate in the receptor site and to find the local energy minimum of the inhibitor-enzyme interaction. Does anyone know how to use the Sybyl(Tripos) or FirstDiscovery(Schrodinger) to do this simulation? I will summarize the suggestions on the list. > > Emilio X. E. ( J. Molecular Graphics and Modelling 18, 283-289, 2000) has > conducted energy minimization after docking. Their method was: the side > chains of the active site and the inhibitor were allowed to relax while > the rest of the receptor including the backbone of the active site were > fixed. > Thanks, Mingzhu -- -------------------------- Mingzhu Zheng Department of chemistry Southern Methodist University Dallas, TX 75275 -------------------------- From chemistry-request@server.ccl.net Thu Jan 23 20:21:41 2003 Received: from father.chem.ubc.ca ([137.82.7.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0O1Lee01261 for ; Thu, 23 Jan 2003 20:21:40 -0500 Received: from localhost (sacooke@localhost) by father.chem.ubc.ca (8.12.5/8.12.6) with ESMTP id h0O1MIG3028074 for ; Thu, 23 Jan 2003 17:22:18 -0800 Date: Thu, 23 Jan 2003 17:22:18 -0800 (PST) From: Stephen Cooke To: chemistry@ccl.net Subject: Electron density at nucleus/field shift In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here is my situation. In a 1982 paper by Knockel et al. (Chem. Phys. 68, 1982, pages 21-28) the authors employed a Hartree-Fock method to determine, for lead sulfide (PbS), the derivative of the electron density at the Pb nucleus with respect to the internuclear separation and then evaluate this derivative at the equilibrium bond length. I would like to perform the same calculation for a number of other heavy metal containing diatomics. To do this I have used g98 with the following input as a test of my method: # uhf/LANL1DZ Density=Current Cube=101 TEST PbS 0 1 Pb 0.0 0.0 0.0 S 2.1 0.0 0.0 pbi.cub I run this input 10 times, each time with a different Pb-S bond length. (As you can see its a very simple calc. and it doesnt take long to run). > From each output I extract the electron density at the Pb nucleus from the grid using a short FORTRAN code. In this extraction it is necessary for me to fit a polynomial to the data and then interpolate for the result at the Pb nucleus. I then fit a polynomial to the data (internuclear separation vs. electron density at the nucleus) take the derivative of the fitted equation and evaluate this derivative at the equilibrium bond length (2.2851). In doing this i get the number -8.984E-05 and i believe the units are bohr^-4. The value quoted by Knockel et al. is closer to +40 angstroms^-4 (!). In my calculation the elec.density at the Pb nucleus is small and from the gradient is clearly decreasing over the increasing internuclear separation I have examined (2.1 - 2.6 angstroms). Knockels results indicate the exact opposite! My assumption is that i am doing the calculation incorrectly (Im a bit green at this). I also have some uncertainties i.e. Is the density that im calculating including the core electrons (nb. I get the same answer as above if i use the core=full keyword), will the effective core potential for Lead affect my results? My ultimate aim, like Knockel et al., is to evaluate the extent of field shift effects upon the rotational energy of a diatomic molecule. With respect to calculating the above I really only need ball park estimates / trends to help me analyse our experimental data. I would be very grateful of any help that anybody could offer and will of course summarise any responses i receive. Steve Cooke sacooke@chem.ubc.ca